Coral Skeletons and Ocean Models Reveal Hidden Decades of Change in the Indonesian Seas

Deep beneath the surface of the Indonesian seas, one of the most consequential chokepoints in the global ocean circulation system has been quietly shifting its thermal and salinity structure for decades, and until now, scientists have had almost no way to see it. A new study published in Climate Dynamics by Sujata A. Murty of the University at Albany and Woods Hole Oceanographic Institution, together with Caroline C. Ummenhofer, Shawn Wang, Laura Gruenburg, Janet Sprintall, Arne Biastoch, Claus W. Böning and colleagues, has pieced together a picture of multi-decadal variability in this critical gateway by fusing two very different kinds of evidence: the chemical archives locked inside long-lived corals and high-resolution ocean model simulations. The result is one of the most detailed reconstructions yet of how temperature and salinity have varied in the upper ocean of the Indonesian Throughflow region across the twentieth century, a period for which direct measurements are sparse to nonexistent.

The Indonesian seas occupy a unique position in the Earth’s climate engine. Warm, low-salinity water from the tropical Pacific flows through the narrow straits and deep channels of the Malay Archipelago and spills into the Indian Ocean, a movement known as the Indonesian Throughflow. This interbasin exchange modulates the global thermohaline circulation, redistributes heat between ocean basins, and influences everything from Indian Ocean dipole events to the pace of global surface warming. Yet the observational network in the region remains thin, and before the intensive INSTANT mooring program of 2004 to 2006 and subsequent Makassar Strait moorings, sustained measurements of throughflow transport and upper-ocean structure were essentially absent. That observational gap has made it extraordinarily difficult to determine whether recent changes in the region are part of natural multi-decadal variability or something new.

The research team’s solution was to turn to corals. Massive coral colonies growing in the main pathways of the Indonesian Throughflow, including sites in the Makassar Strait and near Lombok Strait, incorporate oxygen isotopes into their calcium carbonate skeletons in proportion to the temperature and isotopic composition of the seawater in which they grow. Because coral δ18O responds to both sea surface temperature and sea surface salinity, these skeletons act as natural recorders of the upper-ocean environment, layer by layer, year by year, extending back well before any instrument touched the water. Paired with independent coral Sr/Ca measurements, which isolate the temperature signal, the δ18O records can be deconvolved to reconstruct past salinity variations with remarkable fidelity. The team synthesized coral δ18O records from sites directly within the throughflow pathways, drawing on compilations such as the CoralHydro2k database of tropical hydroclimate proxies.

To interpret what the corals were recording, the researchers turned to eddy-active ocean model simulations performed with the NEMO modeling framework at the North-German Supercomputing Alliance and the Computing Centre at Kiel University. These simulations were driven by the JRA55-do atmospheric reanalysis dataset from the Japan Meteorological Agency, providing realistic surface forcing of winds, heat fluxes, and freshwater inputs. Crucially, the model’s simulated upper-ocean temperature and salinity variability showed consistency with the limited observational data available near the coral sites, including the Labani Channel mooring observations in Makassar Strait. This validation step is what makes the proxy-model synthesis approach credible: if the model reproduces the observed variability where observations exist, then the model can be trusted to fill in the spatial and temporal gaps where corals and instruments cannot.

The comparison between coral records and model output yielded a striking result. On multi-decadal timescales, coral δ18O co-varies with simulated salinity and with the depth of the thermocline, the boundary layer separating warm surface waters from cooler deep waters. This coupling means the corals are not merely recording surface conditions but are sensitive to the vertical structure of the upper ocean, including how deep the warm layer extends. Thermocline depth in the Indonesian seas is controlled by a delicate balance of wind-driven processes in both the Pacific and Indian Oceans, monsoon dynamics, and buoyancy fluxes from rainfall and evaporation. The fact that a surface-dwelling organism’s skeleton tracks this subsurface structure opens a window onto vertical ocean variability that no other proxy archive in the region can provide.

To disentangle the physical drivers, the team ran model sensitivity experiments that separated wind forcing from buoyancy forcing, allowing them to attribute simulated variability to each mechanism independently. The verdict was clear: wind forcing dominates the multi-decadal variability of upper-ocean temperature and salinity structure in the Indonesian seas, with buoyancy forcing, driven by changes in rainfall, evaporation, and surface heat fluxes, contributing episodically throughout the twentieth century. Winds exert their influence by piling up or drawing down water across the basin, modulating the pressure gradient that drives the throughflow and adjusting the depth of the thermocline through Ekman pumping and planetary wave dynamics. This finding aligns with earlier work showing that Pacific trade wind variations, tied to the Interdecadal Pacific Oscillation, exert remote control over Indian Ocean heat content and sea level.

Indeed, the Interdecadal Pacific Oscillation emerges as a central character in this story. Both the coral-reconstructed and simulated variability show sensitivity to the phase changes of this basin-scale climate mode, which alternates between states resembling persistent El Niño and persistent La Niña conditions over the Pacific. When the IPO shifts phase, the winds over the tropical Pacific and the Maritime Continent reorganize, and the consequences propagate through the Indonesian seas as changes in throughflow transport, surface salinity, and thermocline depth. The study highlights that these IPO-related impacts extend beyond the well-documented interannual ENSO teleconnections into the realm of multi-decadal modulation of the regional thermohaline vertical structure, a dimension of variability that short observational records simply cannot capture.

Perhaps the most consequential finding is that the recent multi-decadal modulation of wind-driven surface freshwater operates through fundamentally different mechanisms than those acting at interannual timescales. In other words, the processes that make the Indonesian seas fresher or saltier from one decade to the next are not simply scaled-up versions of the processes that drive year-to-year swings. This non-stationarity has profound implications for how scientists interpret both modern observations and paleoclimate proxies, and for how climate models should be evaluated against the region’s hydrological evolution. As the Indo-Pacific freshwater pool expands under global warming and the global water cycle intensifies, understanding which mechanisms govern freshwater delivery through the Indonesian seas becomes essential for projecting future changes in interbasin heat and salt exchange.

The study’s methodological achievement deserves emphasis as much as its physical findings. By demonstrating that coral δ18O records from throughflow pathways can be meaningfully compared against eddy-resolving model simulations, and that the two archives agree where they overlap, the team has established a template for future proxy-model syntheses in data-sparse ocean regions. The approach transforms corals from isolated curiosity into quantitative constraint, and transforms models from tools of the present into instruments for interrogating the past. As the authors note, future proxy-model comparison will be critical for evaluating whether the drivers of variability they identified persist or shift as Indo-Pacific heat and freshwater exchange continues to evolve far beyond the reach of the short observational record.

For a region that regulates the flow of heat between two of the world’s largest ocean basins, the Indonesian seas have long been under-observed and under-appreciated in the public imagination. This work changes that. It shows that the skeletons of corals growing in Indonesian waters carry a legible, century-scale record of how winds and rains have reshaped the ocean’s vertical architecture, and that state-of-the-art ocean models can read that record and extend it. As climate change accelerates the intensification of the global water cycle and reshapes Pacific wind systems, the multi-decadal memory preserved in coral reefs and reproduced in simulations offers one of the few reliable guides to what the Indonesian Throughflow has done, and what it may do next, in the service of the planet’s climate.

Subject of Research: Multi-decadal upper-ocean temperature and salinity variability in the Indonesian seas reconstructed from coral δ18O records and ocean model simulations

Article Title: Drivers of multi-decadal upper-ocean thermal and haline structure in the Indonesian seas: a synthesis of coral δ18O and ocean models

Article References: Murty, S. A., Ummenhofer, C. C., Wang, S., Gruenburg, L., Sprintall, J., Biastoch, A., & Böning, C. W. (2026). Drivers of multi-decadal upper-ocean thermal and haline structure in the Indonesian seas: a synthesis of coral δ18O and ocean models. Climate Dynamics, 64(10), Article 440. https://doi.org/10.1007/s00382-026-08394-8

Image Credits: AI Generated

DOI: 10.1007/s00382-026-08394-8

Keywords: Indonesian Throughflow, coral δ18O, paleoceanography, ocean modeling, Interdecadal Pacific Oscillation, thermocline, sea surface salinity, Makassar Strait, climate variability, NEMO model, freshwater flux, Indo-Pacific climate